Fetch public data at GEO and analyse it with IPA (GSE72005)

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This page was used to generate data for IPA, for a more complete overview of GEO and public microarray data analysis, please refer to our training pages (http://wiki.bits.vib.be/index.php/Hands-on_Analysis_of_public_microarray_datasets)

Microarray chip used

this last info is necessary when uploading in IPA

Quick differential analysis of the GEO dataset GSE72005

• Go to the following web page http://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE72005

• define groups based on annotations

• control that the signal distribution after normalisation is equivalent for all samples (if very different, abort here!!)

• control which statistical choices have been made

• start data analysis (takes about one minute)

• save full table to your local disk

• when the obtained data looks OK, save it to a text file from your browser

• take a look (and copy) the R-code that you can use as a starter to go further in RStudio (see tutorial linked above)

• re-open the text file in excel (using 'file' 'open') and perform data check as shown below to ensure integrity

• save the excel file and use it in IPA

• launch IPA, login and create a new project to store your data

• upload the excel file

• set the context and background according to what the data is then identify all columns you will need in IPA (ID, logFC, and p-values)

• play with stringency to obtain less tan 600 genes retained and a nice specificity

• for each saved dataset, run a separate core analysis

download exercise files

Download exercise files here.

Use the right application to open the files present in GSE72005-files

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References:

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